Isolation and characterization of the diastereoisomers of a series of phosphate-ethylated dinucleoside monophosphates

Cytotoxic and mutagenic properties of alkyl phosphotriester lesions in Escherichia coli cells

Exposure to many endogenous and exogenous agents can give rise to DNA alkylation, which constitutes a major type of DNA damage. Among the DNA alkylation products, alkyl phosphotriesters have relatively high frequencies of occurrence and are resistant to repair in mammalian tissues. However, little is known about how these lesions affect the efficiency and fidelity of DNA replication in cells or how the replicative bypass of these lesions is modulated by translesion synthesis DNA polymerases. In this study, we synthesized oligodeoxyribonucleotides containing four pairs (S_p and R_p) of alkyl phosphotriester lesions at a defined site, and examined how these lesions are recognized by DNA replication machinery in Escherichia coli cells. We found that the S_p diastereomer of the alkyl phosphotriester lesions could be efficiently bypassed, whereas the R_p counterparts moderately blocked DNA replication. Moreover, the S_p-methyl phosphotriester induced TT→GT and TT→GC mutations at the flanking TT dinucleotide site, and the induction of these mutations required Ada protein, which is known to remove efficiently the methyl group from the S_p-methyl phosphotriester. Together, our study provided a comprehensive understanding about the recognition of alkyl phosphotriester lesions by DNA replication machinery in cells, and revealed for the first time the Ada-dependent induction of mutations at the S_p-methyl phosphotriester site.

Detection of phosphodiester adducts formed by the reaction of benzo[a]pyrene diol epoxide with 2'-deoxynucleotides using collision-induced dissociation electrospray ionization tandem mass spectrometry

In this study, we investigated the products formed following the reaction of benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (B[a]PDE) with 2'-deoxynucleoside 3'-monophosphates. The B[a]PDE plus 2'-deoxynucleotide reaction mixtures were purified using solid phase extraction (SPE) and subjected to HPLC with fluorescence detection. Fractions corresponding to reaction product peaks were collected and desalted using SPE prior to analysis for the presence of molecular ions corresponding to m/z 648, 632, 608 and 623 [M-H]- consistent with B[a]PDE adducted (either on the base or phosphate group) 2'-deoxynucleotides of guanine, adenine, cytosine and thymine, respectively, using LC-ESI-MS/MS collision-induced dissociation (CID). Reaction products were identified having CID product ion spectra containing product ions at m/z 452, 436 and 412 [(B[a]Ptriol+base)-H]-, resulting from cleavage of the glycosidic bond between the 2'-deoxyribose and base, corresponding to B[a]PDE adducts of guanine, adenine and cytosine, respectively. Further reaction products were identified having unique CID product ion spectra characteristic of B[a]PDE adduct formation with the phosphate group of the 2'-deoxynucleotide. The presence of product ions at m/z 399 and 497 were observed for all four 2'-deoxynucleotides, corresponding to [(B[a]Ptriol+phosphate)-H]- and [(2'-deoxyribose+phosphate+B[a]Ptriol)-H]-, respectively. In conclusion, this investigation provides the first direct evidence for the formation of phosphodiester adducts by B[a]PDE following reaction with 2'-deoxynucleotides.

Differences in replication of a DNA template containing an ethyl phosphotriester by T4 DNA polymerase and Escherichia coli DNA polymerase I

A DNA template containing a single ethyl phosphotriester was replicated in vitro by the bacteriophage T4 DNA polymerase and by Escherichia coli DNA polymerase I (DNA pol I). Escherichia coli DNA pol I bypassed the lesion efficiently, but partial inhibition was observed for T4 DNA polymerase. The replication block produced by the ethyl phosphotriester was increased at low dNTP concentrations and for a mutant T4 DNA polymerase with an antimutator phenotype, increased proofreading activity, and reduced ability to bind DNA in the polymerase active center. These observations support a model in which an ethyl phosphotriester impedes primer elongation by T4 DNA polymerase by decreasing formation of the ternary DNA polymerase-DNA-dNTP complex. When primer elongation is not possible, proofreading becomes the favored reaction. Apparent futile cycles of nucleotide incorporation and proofreading, the idling reaction, were observed at the site of the lesion. The replication block was overcome by higher dNTP concentrations. Thus, ethyl phosphotriesters may be tolerated in vivo by the up-regulation of dNTP biosynthesis that occurs during the cellular checkpoint response to blocked DNA replication forks.

Conformational studies of dithymidine boranomonophosphate diastereoisomers

The boranophosphate ester nucleotides are a new class of nucleic acid analogues that are isoelectronic and isostructural to normal phosphodiester nucleic acids and that maintain the anionic charge of the nucleic acid backbone. The two P-diastereoisomers of dithymidine boranomonophosphates were separated using reverse phase HPLC; the faster and slower eluting isomers are designated as d(TpBT)-1 and d(TpBT)-2, respectively. Conformations of the isomers were studied using-circular dichroism (CD) and NMR, and compared to the analogous phosphate diester, d(TpT). This comparison allowed the effects of the borane group and chirality of the boranophosphate linkage on sugar and base conformations to be assessed. The CD spectra of the diastereoisomers are consistent with both having a B-type conformation. Analysis of the 1H-1H and 1H-31P coupling constants showed that these conformations are similar to those of the unmodified parent dimer; specifically, the 2'-deoxyribose rings prefer the S (C2'-endo) conformation, and the C4'-C5' and C5'-O5' rotamers are primarily in the gamma + and beta + conformations, respectively. Conformational differences between the diastereoisomers and between the modified and unmodified dimers are manifested by differences in the preferences of the 3'-residues to adopt S sugar pucker and beta + conformations. There is reduced preference for the S sugar pucker of the 3'-residue in d(TpBT)-1 relative to d(TpBT)-2, which is similar to d(TpT). There is less preference for the beta + conformation of the 3'-residue in d(TpBT)-2 relative to d(TpBT)-1 and d(TpT). Based on the CD results, the temperature dependences of the thymidine H6 chemical shifts, and the derived sugar ring and backbone conformational parameters, we conclude that the borane group exerts a minimal influence on the sugar conformations and base stacking interactions. Preliminary assignment of the absolute configuration of the pair of SP and RP diastereoisomers to d(TpBT)-1 and d(TpBT)-2, respectively, is made on the basis of enzyme selectivity and NOE difference experiments.

Optimization of the separation of the Rp and Sp diastereomers of phosphate-methylated DNA and RNA dinucleotides

The separation by reversed-phase high-performance liquid chromatography of Rp and Sp diastereomers of phosphate-methylated DNA and RNA dinucleotides was studied with respect to pH, organic modifier type and concentration and reversed-phase packing material. Drylab G was used to deduce optimum conditions. On the basis of the observed discrepancies between the computer predictions and experimental results, the gradient operation procedure with volatile buffers was improved. By repetitive chromatography on a 250 x 22 mm I.D. reversed-phase column, fourteen diastereomeric pairs were obtained in at least 97% purity and 60% yield, in amounts of 10-100 mg.